Serotype Distribution Research Articles

Serotype Distribution and Antimicrobial Resistance of Streptococcus pneumoniae Causing Invasive Pneumococcal Disease in Korea Between 2017 and 2019 After Introduction of the 13-Valent Pneumococcal Conjugate Vaccine.

Streptococcus pneumoniae is a serious pathogen causing various infections in humans. We evaluated the serotype distribution and antimicrobial resistance of S. pneumoniae causing invasive pneumococcal disease (IPD) after introduction of pneumococcal conjugate vaccine (PCV)13 in Korea and investigated the epidemiological characteristics of multidrug-resistant (MDR) isolates. S. pneumoniae isolates causing IPD were collected from 16 hospitals in Korea between 2017 and 2019. Serotyping was performed using modified sequential multiplex PCR and the Quellung reaction. Antimicrobial susceptibility tests were performed using the broth microdilution method. Multilocus sequence typing was performed on MDR isolates for epidemiological investigations. Among the 411 S. pneumoniae isolates analyzed, the most prevalent serotype was 3 (12.2%), followed by 10A (9.5%), 34 (7.3%), 19A (6.8%), 23A (6.3%), 22F (6.1%), 35B (5.8%), 11A (5.1%), and others (40.9%). The coverage rates of PCV7, PCV10, PCV13, and pneumococcal polysaccharide vaccine (PPSV)23 were 7.8%, 7.8%, 28.7%, and 59.4%, respectively. Resistance rates to penicillin, ceftriaxone, erythromycin, and levofloxacin were 13.1%, 9.2%, 80.3%, and 4.1%, respectively. MDR isolates accounted for 23.4% of all isolates. Serotypes 23A, 11A, 19A, and 15B accounted for the highest proportions of total isolates at 18.8%, 16.7%, 14.6%, and 8.3%, respectively. Sequence type (ST)166 (43.8%) and ST320 (12.5%) were common among MDR isolates. Non-PCV13 serotypes are increasing among invasive S. pneumoniae strains causing IPD. Differences in antimicrobial resistance were found according to the specific serotype. Continuous monitoring of serotypes and antimicrobial resistance is necessary for the appropriate management of S. pneumoniae infections.

Streptococcus pneumoniae Causing Invasive Diseases in Children and Adults in Central Thailand, 2012-2016.

Longitudinal data regarding the serotype distribution and antimicrobial susceptibility of S. pneumoniae-causing invasive pneumococcal disease (IPD) in developing countries are limited. Our aim was to monitor the antimicrobial susceptibility, serotype distribution, and serotype coverage rates of the pneumococcal conjugate vaccines (PCVs) and emerging non-vaccine serotypes (NVT) between 2012 and 2016 in central Thailand. Pneumococcal isolates from sterile specimens of patients, collected within a long-standing collaborative hospital network in central Thailand between 2012 and 2016, were studied. The pneumococcal serotypes included in the 15-valent PCV were identified by the quellung reaction, while the non-PCV15 serotypes were identified by multiplex PCR. Antimicrobial susceptibilities were determined by the microbroth dilution or disk diffusion method. Of the 276 pneumococcal isolates, 129 (46.7%) were from children aged ≤5 years. Only 9.0% of patients with available data received the PCV prior to the onset of the IPD. The most common vaccine serotypes were 6B (17.4%), 19A (13.0%), and 14 (11.2%), respectively. Non-PCV15 serotypes were detected in 27.9%; the most common serotypes were 15B/C (5.1%), 15A/F (4.0%), and 23A (3.6%), respectively. The serotype coverage rates of PCV10 in children aged ≤5 years was 55.8%, and 53.3% across all ages. PCV13 provided similar coverage rates to that of PCV15, 71.3% in children aged ≤5 years, and 72.1% across all ages. High susceptibilities to cefotaxime (94.6%), ofloxacin (98.2%), linezolid (99.6%), and vancomycin (100.0%) were observed, while the susceptibility to erythromycin (50.0%), TMP-SMZ (41.3%), and tetracycline (27.2%) were low. The susceptibilities to penicillin, meropenem, and clindamycin were 85.9%, 85.9%, and 84.8%, respectively. Serotype 19A was associated with a lower susceptibility than the non-19A isolates for penicillin (75.0% vs. 87.5%, p = 0.045), meropenem (52.8% vs. 90.8%, p < 0.001), erythromycin (33.3% vs. 53.8%, p = 0.022), and TMP-SMZ (16.7% vs. 45.0%, p = 0.001). Although the majority of the pneumococcal serotypes causing IPD in central Thailand were covered by the currently available PCVs, 25% of IPD were caused by NVT. Several emerging NVT identified were 15B/C, 15A/F, and 23A. The high rates of resistance to penicillin, meropenem, erythromycin, TMP-SMZ, and tetracycline observed is a major concern. Serotype 19A was associated with lower antimicrobial susceptibilities in comparison to the non-19A serotypes.

Characterization of Streptococcus pneumoniae Macrolide Resistance and Its Mechanism in Northeast China over a 20-Year Period.

ABSTRACTDue to the resistance of Streptococcus pneumoniae to β-lactams, macrolides, and tetracyclines, treatment alternatives have become increasingly limited worldwide. We aim to describe the characterization of erythromycin-resistant S. pneumoniae (ERSP) strains in northeastern China over a period of 20 years. A total of 1,240 ERSP strains were collected and classified into five groups based on the ages of the patients. Etest strips and Kirby-Bauer disk diffusion were performed for drug susceptibility testing. The capsule swelling test was used for capsule typing. The phenotype of drug resistance was detected by the erythromycin and clindamycin double-disk method. The ermB, ermTR, mefA, and tetM genes were detected by PCR. Among the 1,240 ERSP strains, 510 were invasive isolates, and 730 were noninvasive isolates. The results of drug susceptibility testing showed that the rates of resistance to penicillin, amoxicillin, cefotaxime, ceftriaxone, meropenem, tetracycline, trimethoprim-sulfamethoxazole, and chloramphenicol varied among the different age groups. 19F, 19A, 23F, 14, and 6B were the serotypes that were commonly found among ERSP strains. Among all strains, 99.03% (1,228/1,240) exhibited an MLSB (macrolide-lincosamide-streptogramin B) resistance phenotype, of which 1,221 strains displayed a constitutive MLSB (cMLSB) phenotype and 7 strains showed an inducible MLSB (iMLSB) phenotype. All of these strains carried the ermB gene. In contrast, only 0.97% of strains of M phenotypes were found to carry the mefA gene. Both the ermB and mefA genes were detected in 704 strains that exhibited multidrug resistance, whereas the ermTR gene was not detected. Furthermore, 1,185 tetracycline-resistant strains were found to carry the tetM gene. Macrolide antimicrobial drugs should be used cautiously for the empirical treatment of S. pneumoniae infections.IMPORTANCE This study presents a retrospective analysis using 1,240 clinical erythromycin-resistant Streptococcus pneumoniae (ERSP) isolates collected in northeastern China between January 2000 and December 2019. The serotype distribution, corresponding vaccine coverage, as well as resistance phenotypes, genes, and mechanisms to macrolide and tetracycline of these isolates were systematically described, analyzed, and discussed. We hope that this study will inform clinicians in their respective regions when selecting antimicrobial agents. We also hope that this study is useful for researchers in related fields. Finally, we emphasize in this study that vaccination is the best preventive measure for S. pneumoniae infection considering its resistance to commonly used antibiotics. The determination of the S. pneumoniae serotype distribution also provides valuable empirical evidence for local health authorities when introducing appropriate vaccines in a specific area.

Serotype analysis of pediatric enteroviral meningitis in Gwangju, Republic of Korea: Number of annual cases, distribution by age group, and characteristics of each serotype.

Enteroviral meningitis is a common disease in children; however, serotype data are still lacking, especially for late childhood. This study analyzed the number of annual cases, distribution by age group, and characteristics of each serotype among children with enteroviral meningitis. After the initial screening of 1,009 children (<18 years) with viral meningitis between 2008 and 2021, the data of enteroviral meningitis were retrospectively reviewed. The number of annual cases and serotypes were investigated. The distribution of serotypes across different ages was reviewed. Clinical characteristics of the major serotypes (detected in at least 15 patients) were further examined. Among the 700 patients with enteroviral meningitis, serotypes were tested in 517 patients (73.9%), which could be typed in 370 patients (71.6%). EV-A71 was the most common serotype detected in 2010, 2012, and 2019. After 2020, enterovirus was rarely detected. The group B coxsackieviruses (CVBs) were commonly detected in neonates (CVB1, 33.3%) and infants (CVB5, 17.4%). The echoviruses were commonly detected beyond infancy; E30 was the most frequently detected in late childhood (14.4%) and adolescents (15.4%). EV-A71 was the most frequently detected in early childhood (17.2%). Between the 11 major serotypes, vomiting, headache, and irritability were more commonly associated with echoviruses (P <0.01). In EV-A71, neurologic symptoms and skin lesions were more common (P <0.01). The CVBs were commonly detected in neonates and infants, whereas the echoviruses were commonly detected beyond infancy and caused vomiting, headache, and irritability. EV-A71 was the most frequently detected in early childhood, frequently causing neurologic and dermatologic problems.

Development and Validation of a Sensitive and Robust Multiplex Antigen Capture Assay to Quantify Streptococcus pneumoniae Serotype-Specific Capsular Polysaccharides in Urine.

ABSTRACTStreptococcus pneumoniae is a major cause of community-acquired pneumonia (CAP) in young children, older adults, and those with immunocompromised status. Since the introduction of pneumococcal vaccines, the burden of invasive pneumococcal disease caused by vaccine serotypes (STs) has decreased; however, the effect on the burden of CAP is unclear, potentially due to the lack of testing for pneumococcal STs. We describe the development, qualification, and clinical validation of a high-throughput and multiplex ST-specific urine antigen detection (SSUAD) assay to address the unmet need in CAP pneumococcal epidemiology. The SSUAD assay is sensitive and specific to the 15 STs in the licensed pneumococcal conjugate vaccine V114 (STs 1, 3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F, 22F, 23F, and 33F) and uses ST-specific monoclonal antibodies for rapid and simultaneous quantification of the 15 STs using a Luminex microfluidics system. The SSUAD assay was optimized and qualified using healthy adult urine spiked with pneumococcal polysaccharides and validated using culture-positive clinical urine samples (n = 34). Key parameters measured were accuracy, precision, sensitivity, specificity, selectivity, and parallelism. The SSUAD assay met all prespecified validation acceptance criteria and is suitable for assessments of disease burden associated with the 15 pneumococcal STs included in V114.IMPORTANCE Streptococcus pneumoniae has more than 90 serotypes capable of causing a range of disease manifestations, including otitis media, pneumonia, and invasive diseases, such as bacteremia or meningitis. Only a minority (<10%) of pneumococcal diseases are bacteremic with known serotype distribution. Culture and serotyping of respiratory specimens are neither routine nor reliable. Hence, the serotype-specific disease burden of the remaining (>90%) noninvasive conditions is largely unknown without reliable laboratory techniques. To address this need, a 15-plex urine antigen detection assay was developed and validated to quantify pneumococcal serotype-specific capsular polysaccharides in urine. This assay will support surveillance to estimate the pneumococcal disease burden and serotype distribution in nonbacteremic conditions. Data obtained from this assay will be critical for understanding the impact of pneumococcal vaccines on noninvasive pneumococcal diseases and to inform the choice of pneumococcal serotypes for next-generation vaccines.

Genomic characterization of Tenacibaculum maritimum O-antigen gene cluster and development of a multiplex PCR-based serotyping scheme.

Tenacibaculum maritimum is a devastating bacterial pathogen affecting a large variety of marine fish species. It is responsible for significant economic losses in aquaculture farms worldwide. Different typing methods have been proposed to analyse bacterial diversity and population structure. Serological heterogeneity has been observed and up to four different serotypes have been described so far. However, the underlying molecular factors remain unknown. By combining conventional serotyping and genome-wide association study, we identified the genomic loci likely involved in the O-antigen biosynthesis. This finding allowed the development of a robust multiplex PCR-based serotyping scheme able to detect subgroups within each serotype and therefore performs better than conventional serotyping. This scheme was successfully applied to a large number of isolates from worldwide origin and retrieved from a large variety of fish species. No obvious correlations were observed between the mPCR-based serotype and the host species or the geographic origin of the isolates. Strikingly, the distribution of mPCR-based serotypes does not follow the core genome phylogeny. Nevertheless, this simple and cost-effective mPCR-based serotyping method could be useful for different applications such as population structure analysis, disease surveillance, vaccine formulation and efficacy follow-up.

Pneumococcal nasopharyngeal carriage in children under 5 years of age at an outpatient healthcare facility in Novi Sad, Serbia during the COVID-19 pandemic

ObjectivesTo assess whether pneumococcal nasopharyngeal carriage among children aged 24–60 months reduced during the coronavirus disease 2019 (COVID-19) pandemic in Novi Sad, Serbia, and to investigate the overall prevalence of carriage, serotype distribution and dominant serotypes 2–3 years after the introduction of pneumococcal conjugate vaccine 10. Design and methodsThis prospective, observational study was conducted in February–March 2020, September–November 2020 and April–June 2021, enabling the comparison of results in the pre-pandemic/early pandemic period with two periods during the COVID-19 pandemic. Pneumococci were identified by standard microbiological methods. Serotype identification was performed using conventional multiplex polymerase chain reaction assays. ResultsAmong 1623 children tested, 515 (31.7%, 95% confidence interval 29.4–34.0%) carried pneumococci. A significant increase in prevalence was found between February–March 2020 and September–November 2020 (P=0.0085), with no difference found between September–November 2020 and April–June 2021 (P=0.0524). Pneumococcal colonization was significantly higher in children who were fully vaccinated and among children who attended day care centres. The dominant serotypes were 15B, 6B, 19F, 11A, 6C, 6A, 3, 23F and 19A, representing 66.4% of all isolates. ConclusionsThis study found that pneumococcal nasopharyngeal carriage in children aged 24–60 months was high before the COVID-19 pandemic, and then increased during the pandemic. This rules out a major role of COVID-19 in the suppression of carriage and, probably, transmission.

Distribution of Serotypes Causing Invasive Pneumococcal Disease in Children From High-Income Countries and the Impact of Pediatric Pneumococcal Vaccination.

The introduction and adoption of pneumococcal conjugate vaccines (PCVs) into pediatric national immunization programs (NIPs) has led to large decreases in invasive pneumococcal disease (IPD) incidence caused by vaccine serotypes. Despite these reductions, the global IPD burden in children remains significant. We collected serotype-specific IPD data from surveillance systems or hospital networks of all 30 high-income countries that met inclusion criteria. Data sources included online databases, surveillance system reports, and peer-reviewed literature. Percentage of serotyped cases covered were calculated for all countries combined and by PCV type in the pediatric NIP. We identified 8012 serotyped IPD cases in children <5 or ≤5 years old. PCV13 serotype IPD caused 37.4% of total IPD cases, including 57.1% and 25.2% for countries with PCV10 or PCV13 in the pediatric NIP, respectively, most commonly due to serotypes 3 and 19A (11.4% and 13.3%, respectively, across all countries). In PCV10 countries, PCV15 and PCV20 would cover an additional 45.1% and 55.6% of IPD beyond serotypes contained in PCV10, largely due to coverage of serotype 19A. In PCV13 countries, PCV15 and PCV20 would cover an additional 10.6% and 38.2% of IPD beyond serotypes contained in PCV13. The most common IPD serotypes covered by higher valency PCVs were 10A (5.2%), 12F (5.1%), and 22F and 33F (3.5% each). Much of the remaining IPD burden is due to serotypes included in PCV15 and PCV20. The inclusion of these next generation PCVs into existing pediatric NIPs may further reduce the incidence of childhood IPD.

Pneumococcal serotypes in adults hospitalized with community-acquired pneumonia in Greece using urinary antigen detection tests: the EGNATIA study, November 2017 – April 2019

ABSTRACT Greece introduced a 13-valent pneumococcal conjugate vaccine (PCV13) into the infant national immunization program in 2010 (3 + 1 schedule until June 2019). Since 2015, PCV13 has been recommended for adults aged 19–64 years with comorbidities and adults ≥65 years sequentially with 23-valent pneumococcal polysaccharide vaccine (PPSV23). We examined pneumococcal serotype distribution among Greek adults aged ≥19 years hospitalized with community-acquired pneumonia (CAP) during November 2017-April 2019. This was an interim analysis of EGNATIA, a prospective study of adult hospitalized CAP in the cities of Ioannina and Kavala. Pneumococcus was identified using cultures, BinaxNow®, serotype-specific urinary antigen detection assays (UAD-1/2). Our analysis included overall 482 hospitalized CAP patients (mean age: 70.5 years; 56.4% male). 53.53% of patients belonged to the highest pneumonia severity index (PSI) classes (IV-V). Pneumococcus was detected in 65 (13.5%) patients, with more than half (57%) of cases detected only by UAD. Approximately two-thirds of pneumococcal CAP occurred in those aged ≥65 years (n = 40, 8.3% of CAP). More than half of pneumococcal CAP (n = 35, 53.8%) was caused by PCV13 serotypes. Most frequently detected PCV13 serotypes were 3, 19A, 23F, collectively accounting for 83% of PCV13 vaccine-type (VT) CAP and 6% of all-cause CAP. Overall, 82.9% of PCV13 VT CAP occurred among persons with an indication (age/risk-based) for PCV13 vaccination. Even with a mature PCV13 childhood immunization program, a persistent burden of PCV13 VT CAP exists in Greek adults. Strategies to increase PCV13 (and higher-valency PCVs, when licensed) coverage in adults should be implemented to reduce the disease burden.

Nasopharyngeal Carriage and Serotype Distribution of Streptococcus pneumoniae in Elderly: A Cross-sectional Study in Turkey.

The incidence and mortality of invasive pneumococcal disease are much higher in people over 65 years compared to the general population. The incidence of the disease and the distribution of serotypes changed with the spread of childhood conjugate pneumococcal vaccines and the use of vaccines in the adult age group. Nasopharyngeal carriage is an important stage in the disease pathogenesis. In this study, we aimed to determine the pneumococcal carriage prevalence and serotype distribution in adults aged ≥ 65 years living in a nursing home. The nasopharyngeal swabs were taken from ≥ 65 years old people living in Narlıdere Nursing Home. The specimens were cultured and pneumococci were isolated according to colony appearance, optochin sensitivity and solubility in bile salts. Pneumococcal serotypes were identified using the capsule swelling reaction. Pneumococcus was isolated in 10 of 341 subjects and the pneumococcal carriage prevalence was 2.9%. Advanced age, immunocompromised status and chronic renal failure were associated with pneumococcal carriage. In multivariate model, having immunocompromised status was significantly associated with carriage. Serotypes/serogroups of pneumococci were 7F, 23F, 10, 11, 15. 17, 20 and 33. The 13 valent conjugated pneumococcal vaccine serotype carriage prevalence was 0.6%. Although pneumococcal colonization in older people is uncommon, most of the isolated serotypes are not PCV13 serotypes. The monitoring of pneumococcal serotypes can offer useful information about the circulation of this pathogen among older people and the potential protective effect of pneumococcal vaccines.

Global Distribution of O Serotypes and Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli Collected From the Blood of Patients With Bacteremia Across Multiple Surveillance Studies.

Extraintestinal pathogenic Escherichia coli (ExPEC) is the leading cause of bacteremia worldwide, with older populations having increased risk of invasive bacterial disease. Increasing resistance to first-line antibiotics and emergence of multidrug-resistant (MDR) strains represent major treatment challenges. ExPEC O serotypes are key targets for potential multivalent conjugate vaccine development. Therefore, we evaluated the O serotype distribution and antibiotic resistance profiles of ExPEC strains causing bloodstream infections across 4 regions. Blood culture isolates from patients aged ≥60 years collected during 5 retrospective E. coli surveillance studies in Europe, North America, Asia-Pacific, and South America (2011-2017) were analyzed. Isolates were O serotyped by agglutination; O genotyping was performed for nontypeable isolates. Antimicrobial susceptibility testing was also conducted. Among 3217 ExPEC blood culture isolates, the most ubiquitous O serotype was O25 (n = 737 [22.9%]), followed by O2, O6, O1, O75, O15, O8, O16, O4, O18, O77 group, O153, O9, O101/O162, O86, and O13 (prevalence of ≥1%). The prevalence of these O serotypes was generally consistent across regions, apart from South America; together, these 16 O serotypes represented 77.6% of all ExPEC bacteremia isolates analyzed. The overall MDR frequency was 10.7%, with limited variation between regions. Within the MDR subset (n = 345), O25 showed a dominant prevalence of 63.2% (n = 218). Predominant O serotypes among ExPEC bacteremia isolates are widespread across different regions. O25 was the most prevalent O serotype overall and particularly dominant among MDR isolates. These findings may inform the design of multivalent conjugate vaccines that can target the predominant O serotypes associated with invasive ExPEC disease in older adults.

Analysis of pneumococcal serotypes distribution to determine a model composition for a Russian pneumococcal conjugate vaccine

Diseases caused by Streptococcus pneumoniae, as well as antibiotic resistance of its serotypes, are the leading cause of death amongst children worldwide. To prevent pneumococcal infection, the population is immunised with conjugate vaccines containing different amounts of polysaccharides of certain serotypes. Development of a full-cycle Russian vaccine is vital because the active pharmaceutical ingredients for the vaccines registered in the Russian Federation are produced abroad, and only the final stages of production of vaccines of this group are performed in the territory of the Russian Federation. Considering the phenomenon of serotype replacement associated with the long-term widespread use of pneumococcal conjugate vaccines, it is necessary to carefully select the serotype composition for the new vaccine. The aim of this work was to analyse the serotype distribution of pneumococci in the Russian Federation and other countries in order to select optimal serotypes for the Russian vaccine for human use, taking into account vaccination schedules for each age group. This review presents an analysis of the pneumococcal serotype distribution in the Russian Federation in the pre-vaccination era, as well as after the introduction of routine vaccination. In addition, the review includes data on the serotype distribution in the Eurasian Economic Union countries. The authors described a model composition containing at least sixteen serotypes. It will increase effectiveness of immune protection of the population, providing a more complete coverage of serotypes, considering their prevalence in the Russian Federation. Based on the analysis, the serotype composition for the sixteen-valent pneumococcal conjugate vaccine is proposed for further production and preclinical and clinical trials. A new Russian pneumococcal conjugate vaccine will ensure vaccination of all population groups within the National Immunisation Schedule of the Russian Federation.

Nasopharyngeal carriage rate, serotype distribution, and antimicrobial susceptibility profile of Streptococcus pneumoniae isolated from children under five years old in Kotabaru, South Kalimantan, Indonesia.

Streptococcus pneumoniae is a bacterial pathogen that colonizes the human nasopharynx. Colonization is frequently reported to be high in young children. In this study, we investigated the nasopharyngeal (NP) carriage rate, serotype distribution, and antibiotic susceptibility of S. pneumoniae in children under five years of age in Kotabaru, South Kalimantan, Indonesia. NP swab specimens were collected from 399 young children (mean age: 30 months) who participated in the Rampa Village Community Health Center, with 74% of the participants being Bajau children. S. pneumoniae was identified using optochin susceptibility and bile solubility tests. Serotyping was performed by sequential multiplex PCR, and antimicrobial susceptibility profiling was performed by disk diffusion and microdilution methods. The NP carriage rate of S. pneumoniae was 45% (180/399). The most commonly serotypes were 6A/6B (18%), followed by 15B/15C (17%), 19F (16%), 34 (8%), and 23F (5%); 46% of them were identified as strains of the PCV13 vaccine type. Additionally, almost half of the pneumococcal isolates were non-susceptible to penicillin (40%), whereas non-susceptibility to tetracycline (36.8%), trimethoprim/sulfamethoxazole (29.7%), erythromycin (16.8%), chloramphenicol (9.7%), and clindamycin (8.6%) was also found. We identified 18% (n=34) of S. pneumoniae isolates as multidrug-resistant (MDR) strains, and serotype 19F was the most common (74%) among them. MDR S. pneumoniae vaccine type strains were dominated by serotype 19F. The implementation of a pneumococcal conjugate vaccine program in Indonesia might reduce MDR strains circulating in the community in the future.

Distribution of cardiomyocyte-selective adeno-associated virus serotype 9 vectors in swine following intracoronary and intravenous infusion.

Limited reports exist regarding adeno-associated virus (AAV) biodistribution in swine. This study assessed biodistribution following antegrade intracoronary and intravenous delivery of two self-complementary serotype 9 AAV (AAV9sc) biologics designed to target signaling in the cardiomyocyte considered important for the development of heart failure. Under the control of a cardiomyocyte-specific promoter, AAV9sc.shmAKAP and AAV9sc.RBD express a small hairpin RNA for the perinuclear scaffold protein muscle A-kinase anchoring protein β (mAKAPβ) and an anchoring disruptor peptide for p90 ribosomal S6 kinase type 3 (RSK3), respectively. Quantitative PCR was used to assess viral genome (vg) delivery and transcript expression in Ossabaw and Yorkshire swine tissues. Myocardial viral delivery was 2-5 × 105 vg/µg genomic DNA (gDNA) for both infusion techniques at a dose ∼1013 vg/kg body wt, demonstrating delivery of ∼1-3 viral particles per cardiac diploid genome. Myocardial RNA levels for each expressed transgene were generally proportional to dose and genomic delivery, and comparable with levels for moderately expressed endogenous genes. Despite significant AAV9sc delivery to other tissues, including the liver, neither biologic induced toxic effects as assessed using functional, structural, and circulating cardiac and systemic markers. These results indicate successful targeted delivery of cardiomyocyte-selective viral vectors in swine without negative side effects, an important step in establishing efficacy in a preclinical experimental setting.

Serotype Distribution and Antimicrobial Resistance Profile of Haemophilus influenzae Isolated from School Children with Acute Otitis Media.

Haemophilus influenzae is a Gram-negative opportunistic bacterial pathogen of the human respiratory tract. This study describes the prevalence, serotype distribution, and susceptibility profiles of H. influenzae strains isolated from the nasopharynx of school children with acute otitis media (AOM) in Banyumas Regency, Central Java, Indonesia. H. influenzae was isolated from nasopharyngeal swab specimens using chocolate agar plates supplemented with IsoVitaleX and bacitracin. Serotyping was performed using quantitative polymerase chain reaction. Antimicrobial susceptibility profiles were determined using a microdilution broth assay. H. influenzae was present in 69.7% of samples (85/122). Nontypeable H. influenzae (NHTi) was the most common serotype (95.3%), followed by H. influenzae type b (3.5%) and H. influenzae type f (1.2%). All the H. influenzae isolates were susceptible to levofloxacin, ceftriaxone, imipenem, meropenem, cefuroxime, and cefixime. Most isolates were susceptible to sparfloxacin (99%), cefepime (99%), amoxicillin/clavulanic acid 2 : 1 (99%), ampicillin/sulbactam 2 : 1 (96%), chloramphenicol (94%), tetracycline (93%), ampicillin (87%), and clarithromycin (82%). Nineteen percent of the isolates were resistant to cotrimoxazole, and 11% of the isolates were resistant to ampicillin. This study showed that H. influenzae carriage among samples was dominated by NTHi and less susceptible to cotrimoxazole.

Serotyping and Seroprevalence of Mannheimia haemolytica, Pasteurella multocida, and Bibersteinia trehalosi and Assessment of Determinants of Ovine Pasteurellosis in West Amhara Sub-region, Ethiopia

A cross-sectional study was undertaken in four (4) districts of the West Amhara sub-region of Ethiopia with the aim of assessing the diversity and distribution of serotypes of Pasteurella species, their seroprevalence, and associated risk factors, and knowledge, attitude, and practice of farmers toward ovine pasteurellosis. A total of 600 sheep sera were collected using multistage cluster sampling. Each sample was examined for the presence of six (6) serotype-specific antibodies using an indirect haemagglutination test. We are reporting a higher seroprevalence of 90.17% (541/600) in which all seropositive animals were shown to have been co-infected with multiple serotypes. Individual serotype prevalence showed that serotype A7 has the highest prevalence of 77.83% followed by A2 (74.33%), T15 (64%), T4 (62%), PA (60%), and A1 (39.17%). In this study, being female [odds ratio (OR): 2.45, 95% CI (1.09–5.52), p = 0.031] and living in high altitude areas [OR: 20.29, 95% CI (2.54–161.95), p = 0.004] were found to be significantly associated with sero-positivity. A questionnaire survey (n = 384) employed in a face-to-face interview was used to assess the knowledge, attitude, and practice of farmers related to ovine pasteurellosis. Accordingly, the majority (72.4%) of respondents had an inadequate knowledge level of the disease. The proportion of farmers with a favorable attitude and good practices toward the disease was 50.26 and 77.6%, respectively. This study is highly indicative that ovine pasteurellosis is a ubiquitous disease in the study area challenging the sheep production sector. The existence of diverse serotypes reported to lack cross-protective immunity is likely to explain why the current vaccination practice with the mono-serotype Pasteurella multocida biotype A vaccine is not providing adequate protection against outbreaks of the disease. Prioritization of one or more serotypes for inclusion in a multivalent vaccine should be dictated by the abundance and distribution of a particular serotype, its clinical importance, and its resultant economic impact. Furthermore, training farmers on key aspects of the disease is vital in the implementation of effective disease management strategies through a participatory approach. Data from the remaining regions of the country could help realize the development of an effective vaccine that works best at the national level.

Effect of childhood vaccination and antibiotic use on pneumococcal populations and genome-wide associations with disease among children in Nepal: an observational study

SummaryBackgroundPneumococcal disease is a leading cause of bacterial pneumonia and invasive bacterial disease among children globally. The reason some strains of pneumococci are more likely to cause disease, and how interventions such as vaccines and antibiotics affect pneumococcal strains is poorly understood. We aimed to identify genetic regions under selective pressure and those associated with disease through the analysis of pneumococcal whole-genome sequences.MethodsWhole-genome sequencing was performed on pneumococcal isolates collected between January, 2005, and May, 2018, in Kathmandu, Nepal, which included programmatic ten-valent pneumococcal conjugate vaccine (PCV10) introduction in 2015. Isolates were from three distinct cohorts: nasopharyngeal swabs of healthy community-based children, nasopharyngeal swabs of children admitted to hospital with pneumonia, and sterile-site cultures from children admitted to hospital. Across these cohorts we examined serotype distribution, antibiotic resistance, strain distribution, and regions of recombination to determine genes that were undergoing diversifying selection. Genome-wide association studies comparing pneumonia and sterile-site isolates with healthy carriage were used to determine novel variants associated with disease.FindingsAfter programmatic introduction of PCV10, there was a decline in vaccine covered serotypes; however, strains that had expressed these serotypes continued to exist in the post-PCV population. We identified GPSC9 to be a strain of concern due to its high prevalence in disease, multidrug resistance, and ability to switch to an unencapsulated phenotype via insertion of virulence factor pspC into the cps locus. Antibiotic resistance loci to co-trimoxazole were found to be prevalent (pre-PCV10 78% vs post-PCV10 81%; p=0·27) and increasingly prevalent to penicillin (pre-PCV10 15% vs post-PCV10 32%; p<0·0001). Regions with multiple recombinations were identified spanning the surface protein virulence factors pspA and pspC and antibiotic targets pbpX, folA, folC, folE, and folP. Furthermore, we identified variants in lacE2 to be strongly associated with isolates from children with pneumonia and PRIP to be strongly associated with isolates from sterile sites.InterpretationOur work highlights the effect of pneumococcal conjugate vaccines, antibiotics, and host–pathogen interaction in pneumococcal variation, and the pathogen's capability of adapting to these factors at both population-wide and strain-specific levels. Ongoing surveillance of disease-associated strains and further investigation of lacE2 and PRIP as serotype-independent targets for therapeutic interventions is required.FundingGavi, The Vaccine Alliance; WHO; Bill & Melinda Gates Foundation; Wellcome Sanger Institute; and US Centers for Disease Control and Prevention.

Genomic Analysis of Group B Streptococcus from Neonatal Sepsis Reveals Clonal CC17 Expansion and Virulence- and Resistance-Associated Traits After Intrapartum Antibiotic Prophylaxis.

Group B Streptococcus (GBS) is a leading cause of invasive neonatal infections. This study aimed to investigate the trend of GBS serotype and genotype change and their correlation with antimicrobial resistance before and after implementation of intrapartum antibiotic prophylaxis (IAP). We performed serotyping, whole-genome sequencing, antimicrobial susceptibility testing, and single-nucleotide polymorphism (SNP)-based phylogenetic analysis on 238 invasive GBS isolates collected from October 1998 to February 2020 in Taiwan. There were 7 serotypes and 6 clonal complexes (CCs) among the 238 GBS isolates, and more than half of the isolates carried multiple antimicrobial resistance genes. The expansion of CC17 strains and the increase in late-onset disease occurred synchronously after the implementation of IAP. Analysis of the carriage isolates from pregnant women showed diverse serotype distribution in the IAP era. The antimicrobial susceptibility testing showed that all 238 strains were susceptible to ampicillin and penicillin, while the number of various resistance genes in GBS genomes was found increased with the expansion of CC17. Compared with reference genomes, 697 nonsynonymous SNPs in 443 protein-coding genes were CC17 specific. The study revealed the expansion of GBS CC17 and the increase of late-onset disease that occurred simultaneously with the implementation of IAP. Although the susceptibility of CC17 to antimicrobial agents is not different from that of other sequence types at present, GBS with phenotypic resistance to antimicrobials may emerge in the future, given the environmental selection pressure and the continued accumulation of SNP mutations.

Dynamic changes in clinical characteristics and serotype distribution of invasive pneumococcal disease among adults in Japan after introduction of the pediatric 13-valent pneumococcal conjugate vaccine in 2013–2019

Nationwide population-based surveillance for invasive pneumococcal disease (IPD) is being conducted in few Asian countries. We aimed to evaluate the clinical characteristics and serotype distribution among Japanese adult patients with IPD after introduction of the pediatric 13-valent pneumococcal conjugate vaccine (PCV13) in 2013. IPD surveillance was conducted among adults between 2013 and 2019, and 1,995 patients were analyzed by time period (early, 2013–2015; middle, 2016–2017; late, 2018–2019). We found that the period of 2018–2019 was independently associated with a lower risk of fatal outcome, compared with the period of 2013–2015. The proportion of those with serotype PCV13-nonPCV7 decreased significantly in patients aged 15–64 years and in those aged ≥ 65 years within 3 years after the introduction of pediatric PCV13. By contrast, the proportion of those with nonvaccine serotype increased significantly in those aged ≥ 65 years, but not in those aged 15–64 years. No significant change was found in the proportion of 23-valent polysaccharide pneumococcal vaccine (PPSV23)-nonPCV13 in both of adults aged 15–64 years and ≥ 65 years. The proportions of PCV15-, PCV20- and PCV24-covered serotypes were 38%, 56% and 58% in adult patients with IPD aged ≥ 65 years during the late period. Our data on the serotype distribution support an indirect effect from pediatric PCV13 use among adults, and afford a basis for estimates of protection against IPD by vaccination with newly developed PCVs in older adults in Japan.

High prevalence of multiple serotypes of pneumococci in patients with pneumonia and their associated risk factors

BackgroundMultiple serotypes of pneumococci have epidemiological and clinical implications, such as the emergence of non-vaccine serotypes and the acquisition of antimicrobial resistance. Prevalence of multiple serotypes of pneumococci in adults...